create_bathy.f90 File Reference

This program creates fine grid bathymetry file. More...

Functions/Subroutines
program	create_bathy
type(tvar) function	create_bathy_matrix (td_var, td_coord)
	This function create variable, filled with matrix value. More...
type(tvar) function	create_bathy_extract (td_var, td_mpp, td_coord)
	This function extract variable from file over coordinate domain and return variable structure. More...
type(tvar) function	create_bathy_get_var (td_var, td_mpp, id_imin, id_jmin, id_imax, id_jmax, id_offset, id_rho)
	This function get coarse grid variable, interpolate variable, and return variable structure over fine grid. More...
subroutine	create_bathy_interp (td_var, id_rho, id_offset, id_iext, id_jext)
	This subroutine interpolate variable. More...
subroutine	create_bathy_check_depth (td_mpp, td_depth)
	This subroutine get depth variable value in an open mpp structure and check if agree with already input depth variable. More...
subroutine	create_bathy_check_time (td_mpp, td_time)
	This subroutine get date and time in an open mpp structure and check if agree with date and time already read. More...

Detailed Description

This program creates fine grid bathymetry file.

method

Bathymetry could be extracted from fine grid Bathymetry file, interpolated from coarse grid Bathymetry file, or manually written.

how to

to create fine grid bathymetry file:

./SIREN/bin/create_bathy create_bathy.nam

Note

you could find a template of the namelist in templates directory.

create_bathy.nam contains 7 namelists:

• logger namelist (namlog)
• config namelist (namcfg)
• coarse grid namelist (namcrs)
• fine grid namelist (namfin)
• variable namelist (namvar)
• nesting namelist (namnst)
• output namelist (namout)

logger namelist (namlog):

• cn_logfile : log filename
• cn_verbosity : verbosity ('trace','debug','info', 'warning','error','fatal','none')
• in_maxerror : maximum number of error allowed

config namelist (namcfg):

• cn_varcfg : variable configuration file (see ./SIREN/cfg/variable.cfg)
• cn_dimcfg : dimension configuration file. defines dimension allowed (see ./SIREN/cfg/dimension.cfg).
• cn_dumcfg : useless (dummy) configuration file, for useless dimension or variable (see ./SIREN/cfg/dummy.cfg).

coarse grid namelist (namcrs):

• cn_coord0 : coordinate file
• in_perio0 : NEMO periodicity index (see Model Boundary Condition in NEMO documentation)

fine grid namelist (namfin):

• cn_coord1 : coordinate file
• in_perio1 : periodicity index
• ln_fillclosed : fill closed sea or not (default is .TRUE.)

variable namelist (namvar):

• cn_varfile : list of variable, and corresponding file.
  cn_varfile is the path and filename of the file where find variable.

  Note

  cn_varfile could be a matrix of value, if you want to filled manually variable value.
  the variable array of value is split into equal subdomain.
  Each subdomain is filled with the corresponding value of the matrix.
  separators used to defined matrix are:

  • ',' for line
  • '/' for row Example:
    3,2,3/1,4,5 =>

  Examples:
  • 'Bathymetry:gridT.nc'
  • 'Bathymetry:5000,5000,5000/5000,3000,5000/5000,5000,5000'

• cn_varinfo : list of variable and extra information about request(s) to be used.
  each elements of cn_varinfo is a string character (separated by ',').
  it is composed of the variable name follow by ':', then request(s) to be used on this variable.
  request could be:

  • int = interpolation method
  • ext = extrapolation method
  • flt = filter method
  • min = minimum value
  • max = maximum value
  • unt = new units

  • unf = unit scale factor (linked to new units)

    requests must be separated by ';'.
    order of requests does not matter.
    

  informations about available method could be find in interp, extrap and filter modules.
  Example: 'Bathymetry: flt=2*hamming(2,3); min=0'

  Note

  If you do not specify a method which is required, default one is apply.

  Warning

  variable name must be Bathymetry here.

nesting namelist (namnst):

• in_rhoi : refinement factor in i-direction
• in_rhoj : refinement factor in j-direction

  Note

  coarse grid indices will be deduced from fine grid coordinate file.

output namelist (namout):

• cn_fileout : output bathymetry file

Author

J.Paul

Function/Subroutine Documentation

program create_bathy

(

)

Date

November, 2013 - Initial Version

Sepember, 2014

• add header for user
• Bug fix, compute offset depending of grid point

June, 2015

• extrapolate all land points.
• allow to change unit.

September, 2015

• manage useless (dummy) variable, attributes, and dimension

January,2016

• add create_bathy_check_depth as in create_boundary
• add create_bathy_check_time as in create_boundary

February, 2016

• do not closed sea for east-west cyclic domain

October, 2016

• dimension to be used select from configuration file

Todo:

• check tl_multi is not empty

Note

Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)

subroutine create_bathy::create_bathy_check_depth	(	type(tmpp), intent(in)	td_mpp,
		type(tvar), intent(inout)	td_depth
	)

This subroutine get depth variable value in an open mpp structure and check if agree with already input depth variable.

Author

J.Paul

Date

January, 2016 - Initial Version

Parameters

[in]	td_mpp	mpp structure
[in,out]	td_depth	depth variable structure

subroutine create_bathy::create_bathy_check_time	(	type(tmpp), intent(in)	td_mpp,
		type(tvar), intent(inout)	td_time
	)

This subroutine get date and time in an open mpp structure and check if agree with date and time already read.

Author

J.Paul

Date

January, 2016 - Initial Version

Parameters

[in]	td_mpp	mpp structure
[in,out]	td_time	time variable structure

type(tvar) function create_bathy::create_bathy_extract	(	type(tvar), intent(in)	td_var,
		type(tmpp), intent(in)	td_mpp,
		type(tmpp), intent(in)	td_coord
	)

This function extract variable from file over coordinate domain and return variable structure.

Author

J.Paul

Date

November, 2013 - Initial Version

Parameters

[in]	td_var	variable structure
[in]	td_mpp	mpp file structure
[in]	td_coord	coordinate file structure

Returns

variable structure

type(tvar) function create_bathy::create_bathy_get_var	(	type(tvar), intent(in)	td_var,
		type(tmpp), intent(in)	td_mpp,
		integer(i4), intent(in)	id_imin,
		integer(i4), intent(in)	id_jmin,
		integer(i4), intent(in)	id_imax,
		integer(i4), intent(in)	id_jmax,
		integer(i4), dimension(:,:), intent(in)	id_offset,
		integer(i4), dimension(:), intent(in)	id_rho
	)

This function get coarse grid variable, interpolate variable, and return variable structure over fine grid.

Author

J.Paul

Date

November, 2013 - Initial Version

Parameters

[in]	td_var	variable structure
[in]	td_mpp	mpp file structure
[in]	id_imin	i-direction lower left corner indice
[in]	id_imax	i-direction upper right corner indice
[in]	id_jmin	j-direction lower left corner indice
[in]	id_jmax	j-direction upper right corner indice
[in]	id_offset	offset between fine grid and coarse grid
[in]	id_rho	array of refinement factor

Returns

variable structure

subroutine create_bathy::create_bathy_interp	(	type(tvar), intent(inout)	td_var,
		integer(i4), dimension(:), intent(in)	id_rho,
		integer(i4), dimension(:,:), intent(in)	id_offset,
		integer(i4), intent(in), optional	id_iext,
		integer(i4), intent(in), optional	id_jext
	)

This subroutine interpolate variable.

Author

J.Paul

Date

November, 2013 - Initial Version

Parameters

[in,out]	td_var	variable structure
[in]	id_rho	array of refinment factor
[in]	id_offset	array of offset between fine and coarse grid
[in]	id_iext	i-direction size of extra bands (default=im_minext)
[in]	id_jext	j-direction size of extra bands (default=im_minext)

type(tvar) function create_bathy::create_bathy_matrix	(	type(tvar), intent(in)	td_var,
		type(tmpp), intent(in)	td_coord
	)

This function create variable, filled with matrix value.

A variable is create with the same name that the input variable, and with dimension of the coordinate file.
Then the variable array of value is split into equal subdomain. Each subdomain is filled with the corresponding value of the matrix.

Author

J.Paul

Date

November, 2013 - Initial Version

Parameters

[in]	td_var	variable structure
[in]	td_coord	coordinate file structure

Returns

variable structure